Multiple sequence alignment - TraesCS7D01G261100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G261100 chr7D 100.000 6956 0 0 1 6956 236817898 236824853 0.000000e+00 12846.0
1 TraesCS7D01G261100 chr7D 94.545 110 6 0 3640 3749 310990196 310990305 3.340000e-38 171.0
2 TraesCS7D01G261100 chr7D 92.771 83 3 2 4706 4786 46702741 46702660 4.410000e-22 117.0
3 TraesCS7D01G261100 chr7D 89.655 87 2 4 4709 4789 5307743 5307658 3.430000e-18 104.0
4 TraesCS7D01G261100 chr7B 96.791 3927 88 14 1 3908 213453941 213457848 0.000000e+00 6519.0
5 TraesCS7D01G261100 chr7B 96.435 2188 24 15 4809 6956 213458716 213460889 0.000000e+00 3559.0
6 TraesCS7D01G261100 chr7B 94.805 847 14 5 3911 4746 213457883 213458710 0.000000e+00 1293.0
7 TraesCS7D01G261100 chr7B 94.595 111 6 0 3639 3749 357651484 357651594 9.280000e-39 172.0
8 TraesCS7D01G261100 chr7B 91.358 81 5 2 4704 4783 18081129 18081208 7.380000e-20 110.0
9 TraesCS7D01G261100 chr7A 97.035 3845 83 11 7 3840 252174775 252178599 0.000000e+00 6440.0
10 TraesCS7D01G261100 chr7A 97.456 1415 24 4 4992 6403 252179563 252180968 0.000000e+00 2403.0
11 TraesCS7D01G261100 chr7A 95.213 773 21 4 3910 4671 252178799 252179566 0.000000e+00 1208.0
12 TraesCS7D01G261100 chr7A 97.213 574 10 4 6387 6956 252181181 252181752 0.000000e+00 966.0
13 TraesCS7D01G261100 chr7A 92.593 81 2 2 4707 4783 68881182 68881102 5.700000e-21 113.0
14 TraesCS7D01G261100 chr7A 94.340 53 3 0 3856 3908 252178713 252178765 1.610000e-11 82.4
15 TraesCS7D01G261100 chr6D 95.370 108 5 0 3638 3745 391925986 391925879 9.280000e-39 172.0
16 TraesCS7D01G261100 chr3D 94.495 109 6 0 3638 3746 379826240 379826348 1.200000e-37 169.0
17 TraesCS7D01G261100 chr3A 94.495 109 6 0 3638 3746 503822394 503822286 1.200000e-37 169.0
18 TraesCS7D01G261100 chr3A 87.912 91 6 3 4703 4790 440634957 440635045 1.230000e-17 102.0
19 TraesCS7D01G261100 chr2D 93.103 116 4 1 3638 3749 307026548 307026663 4.320000e-37 167.0
20 TraesCS7D01G261100 chr2A 92.308 117 9 0 3639 3755 205917600 205917716 4.320000e-37 167.0
21 TraesCS7D01G261100 chr1D 95.946 74 1 2 4713 4784 464799722 464799795 1.230000e-22 119.0
22 TraesCS7D01G261100 chr4D 93.421 76 1 2 4708 4783 40796892 40796821 7.380000e-20 110.0
23 TraesCS7D01G261100 chr2B 91.463 82 3 2 4717 4794 5666173 5666254 7.380000e-20 110.0
24 TraesCS7D01G261100 chr2B 91.026 78 5 1 4714 4789 149844812 149844735 3.430000e-18 104.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G261100 chr7D 236817898 236824853 6955 False 12846.000000 12846 100.000000 1 6956 1 chr7D.!!$F1 6955
1 TraesCS7D01G261100 chr7B 213453941 213460889 6948 False 3790.333333 6519 96.010333 1 6956 3 chr7B.!!$F3 6955
2 TraesCS7D01G261100 chr7A 252174775 252181752 6977 False 2219.880000 6440 96.251400 7 6956 5 chr7A.!!$F1 6949

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
96 97 0.033504 GCTCTGTGAACCGAACCTGA 59.966 55.0 0.00 0.00 0.00 3.86 F
380 387 0.039035 TGGCCGGGAATAGCAACTTT 59.961 50.0 2.18 0.00 0.00 2.66 F
603 610 0.734253 CAGAGAGCCCGTTGAACTCG 60.734 60.0 0.00 0.00 35.56 4.18 F
681 688 1.367659 TCAATGCGATGCACGAATGA 58.632 45.0 11.94 9.12 43.04 2.57 F
2159 2173 1.021202 CGAAGTGCCAAAACACCTCA 58.979 50.0 0.00 0.00 41.67 3.86 F
2223 2237 1.260544 GCCATCAGGAAAACAGGCTT 58.739 50.0 0.00 0.00 39.02 4.35 F
3908 4020 0.179936 GGCCTCCTGGAGTGAATCTG 59.820 60.0 21.70 6.27 34.57 2.90 F
4784 4941 0.186873 TATGGGACGGAGGGAGTACC 59.813 60.0 0.00 0.00 42.94 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 1885 1.109323 GCAAGCTGGGGTGAACACTT 61.109 55.000 4.96 0.0 0.00 3.16 R
2076 2090 2.890945 GGTTCCTGGTGCTGTTTGTTAT 59.109 45.455 0.00 0.0 0.00 1.89 R
2159 2173 3.680458 GCGCAAGTCTAGCTTTAACTTCT 59.320 43.478 0.30 0.0 41.68 2.85 R
2666 2680 5.220491 GCTTGCTTTTAACTGATCTAGTCGG 60.220 44.000 0.00 0.0 39.18 4.79 R
3717 3731 4.283467 CCCTCCGATCCATATTACTTGTCA 59.717 45.833 0.00 0.0 0.00 3.58 R
4085 4229 5.645067 TGCATGACTAAATGTCCTTCAAGAG 59.355 40.000 0.00 0.0 44.75 2.85 R
4845 5002 0.097674 GCGCCTGAAATGCACACTAG 59.902 55.000 0.00 0.0 0.00 2.57 R
6301 6499 3.306472 AAAAGGGTGACTGTTTGCCTA 57.694 42.857 0.00 0.0 0.00 3.93 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 0.033504 GCTCTGTGAACCGAACCTGA 59.966 55.000 0.00 0.00 0.00 3.86
139 140 3.001634 TGAGATCGGACGTCGTTATACAC 59.998 47.826 9.92 0.00 40.32 2.90
270 277 1.167781 AAAACGTGGACGCCGGAAAT 61.168 50.000 5.05 0.00 44.43 2.17
294 301 4.922206 TCAGCAATCCACAAATAGAACCT 58.078 39.130 0.00 0.00 0.00 3.50
368 375 2.918230 GAAGATACCACGTGGCCGGG 62.918 65.000 34.26 11.24 39.32 5.73
380 387 0.039035 TGGCCGGGAATAGCAACTTT 59.961 50.000 2.18 0.00 0.00 2.66
398 405 2.107950 TTCATGCCCAGGAAACTACG 57.892 50.000 0.00 0.00 40.21 3.51
399 406 0.981183 TCATGCCCAGGAAACTACGT 59.019 50.000 0.00 0.00 40.21 3.57
400 407 2.181125 TCATGCCCAGGAAACTACGTA 58.819 47.619 0.00 0.00 40.21 3.57
401 408 2.093869 TCATGCCCAGGAAACTACGTAC 60.094 50.000 0.00 0.00 40.21 3.67
402 409 1.636148 TGCCCAGGAAACTACGTACT 58.364 50.000 0.00 0.00 40.21 2.73
403 410 2.806434 TGCCCAGGAAACTACGTACTA 58.194 47.619 0.00 0.00 40.21 1.82
404 411 2.493278 TGCCCAGGAAACTACGTACTAC 59.507 50.000 0.00 0.00 40.21 2.73
532 539 2.971330 AGCAATCCACATGTCCCAAAAA 59.029 40.909 0.00 0.00 0.00 1.94
603 610 0.734253 CAGAGAGCCCGTTGAACTCG 60.734 60.000 0.00 0.00 35.56 4.18
671 678 5.106555 ACTCATCTTTTCGTTTCAATGCGAT 60.107 36.000 0.00 0.00 36.97 4.58
679 686 2.518949 GTTTCAATGCGATGCACGAAT 58.481 42.857 11.94 4.84 43.04 3.34
680 687 2.177001 TTCAATGCGATGCACGAATG 57.823 45.000 11.94 7.37 43.04 2.67
681 688 1.367659 TCAATGCGATGCACGAATGA 58.632 45.000 11.94 9.12 43.04 2.57
811 818 1.583477 GCTTCAGGCTTTGGCTCAC 59.417 57.895 0.00 0.00 35.88 3.51
914 921 5.447954 CCACTCACTACTTACACATCTCTCG 60.448 48.000 0.00 0.00 0.00 4.04
1023 1035 3.695606 TCACTCAGGACGGCTGGC 61.696 66.667 0.00 0.00 0.00 4.85
1056 1068 4.200283 GCTCTGCCGGAGTCCTCG 62.200 72.222 5.05 0.00 43.62 4.63
1121 1133 1.610522 CCCCAGTTTCTCTTGCACAAG 59.389 52.381 3.94 3.94 39.71 3.16
1299 1312 2.093890 TGCGGATTCAACTGCATCAAT 58.906 42.857 0.00 0.00 45.49 2.57
1396 1410 6.749923 ATAACTCTCAACTGAAGGCATTTC 57.250 37.500 0.00 0.00 36.29 2.17
1398 1412 2.751806 CTCTCAACTGAAGGCATTTCCC 59.248 50.000 0.00 0.00 34.77 3.97
1764 1778 4.323417 TGTTCATCTCACATACCAACCAC 58.677 43.478 0.00 0.00 0.00 4.16
1766 1780 4.632327 TCATCTCACATACCAACCACAA 57.368 40.909 0.00 0.00 0.00 3.33
1871 1885 2.151202 GATCCCTCAAACGTTCTTGCA 58.849 47.619 0.00 0.00 0.00 4.08
2111 2125 4.210331 CCAGGAACCAGGAAAATGATAGG 58.790 47.826 0.00 0.00 0.00 2.57
2112 2126 4.210331 CAGGAACCAGGAAAATGATAGGG 58.790 47.826 0.00 0.00 0.00 3.53
2113 2127 4.079787 CAGGAACCAGGAAAATGATAGGGA 60.080 45.833 0.00 0.00 0.00 4.20
2114 2128 4.733988 AGGAACCAGGAAAATGATAGGGAT 59.266 41.667 0.00 0.00 0.00 3.85
2115 2129 5.917087 AGGAACCAGGAAAATGATAGGGATA 59.083 40.000 0.00 0.00 0.00 2.59
2116 2130 6.044871 AGGAACCAGGAAAATGATAGGGATAG 59.955 42.308 0.00 0.00 0.00 2.08
2159 2173 1.021202 CGAAGTGCCAAAACACCTCA 58.979 50.000 0.00 0.00 41.67 3.86
2223 2237 1.260544 GCCATCAGGAAAACAGGCTT 58.739 50.000 0.00 0.00 39.02 4.35
2344 2358 4.335416 AGTTCCAAACATATCCCACACAG 58.665 43.478 0.00 0.00 0.00 3.66
2450 2464 9.833917 TGGAATATACTAGATACTACGATGGAG 57.166 37.037 0.00 0.00 0.00 3.86
3024 3038 5.371115 TGGACAAAGTCGAAAAATGGATC 57.629 39.130 0.00 0.00 32.65 3.36
3393 3407 6.127310 ACGATGAGGTGAGAGCTTATAACTTT 60.127 38.462 0.00 0.00 0.00 2.66
3908 4020 0.179936 GGCCTCCTGGAGTGAATCTG 59.820 60.000 21.70 6.27 34.57 2.90
4036 4180 1.525535 CTGCTGCTGGTATGGGAGC 60.526 63.158 0.00 0.00 45.98 4.70
4164 4321 5.552178 AGGACTGACATTAACTCTTTGGTC 58.448 41.667 0.00 0.00 0.00 4.02
4223 4380 9.656040 AAATGACAAGCATGAAATTTAGCATTA 57.344 25.926 0.00 0.00 37.28 1.90
4284 4441 9.743057 CAGTAAACAATAAATCCAACAACTGAA 57.257 29.630 0.00 0.00 33.09 3.02
4384 4541 2.571212 CCCCTATAACGCTGCATTTGA 58.429 47.619 0.00 0.00 0.00 2.69
4385 4542 2.948979 CCCCTATAACGCTGCATTTGAA 59.051 45.455 0.00 0.00 0.00 2.69
4386 4543 3.380004 CCCCTATAACGCTGCATTTGAAA 59.620 43.478 0.00 0.00 0.00 2.69
4636 4793 3.462982 TGAGCAACGTGTAACACTGAAT 58.537 40.909 0.00 0.00 35.74 2.57
4674 4831 9.965824 AAATTACAGACTTCAGTTACCATTTTG 57.034 29.630 0.00 0.00 0.00 2.44
4746 4903 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
4748 4905 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
4749 4906 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
4750 4907 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
4751 4908 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
4752 4909 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
4753 4910 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
4754 4911 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
4755 4912 7.582679 CCATAATATAAGAGCGTTTTTGACACG 59.417 37.037 0.00 0.00 40.75 4.49
4768 4925 8.463001 CGTTTTTGACACGCTCTTATATTATG 57.537 34.615 0.00 0.00 0.00 1.90
4769 4926 7.582679 CGTTTTTGACACGCTCTTATATTATGG 59.417 37.037 0.00 0.00 0.00 2.74
4770 4927 7.490962 TTTTGACACGCTCTTATATTATGGG 57.509 36.000 0.00 0.00 0.00 4.00
4771 4928 6.413783 TTGACACGCTCTTATATTATGGGA 57.586 37.500 0.00 0.00 0.00 4.37
4772 4929 5.779922 TGACACGCTCTTATATTATGGGAC 58.220 41.667 0.00 0.00 0.00 4.46
4773 4930 4.806330 ACACGCTCTTATATTATGGGACG 58.194 43.478 0.00 0.00 0.00 4.79
4774 4931 4.174009 CACGCTCTTATATTATGGGACGG 58.826 47.826 0.00 0.00 0.00 4.79
4775 4932 4.082408 CACGCTCTTATATTATGGGACGGA 60.082 45.833 0.00 0.00 0.00 4.69
4776 4933 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
4777 4934 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
4778 4935 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
4779 4936 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
4780 4937 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
4781 4938 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
4782 4939 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
4783 4940 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
4784 4941 0.186873 TATGGGACGGAGGGAGTACC 59.813 60.000 0.00 0.00 42.94 3.34
4785 4942 2.361771 GGGACGGAGGGAGTACCA 59.638 66.667 0.00 0.00 42.20 3.25
4786 4943 1.075450 GGGACGGAGGGAGTACCAT 60.075 63.158 0.00 0.00 42.20 3.55
4787 4944 0.690077 GGGACGGAGGGAGTACCATT 60.690 60.000 0.00 0.00 42.20 3.16
4788 4945 1.201424 GGACGGAGGGAGTACCATTT 58.799 55.000 0.00 0.00 43.89 2.32
4789 4946 2.391678 GGACGGAGGGAGTACCATTTA 58.608 52.381 0.00 0.00 43.89 1.40
4790 4947 2.970640 GGACGGAGGGAGTACCATTTAT 59.029 50.000 0.00 0.00 43.89 1.40
4791 4948 4.154942 GGACGGAGGGAGTACCATTTATA 58.845 47.826 0.00 0.00 43.89 0.98
4792 4949 4.021632 GGACGGAGGGAGTACCATTTATAC 60.022 50.000 0.00 0.00 43.89 1.47
4793 4950 4.812653 ACGGAGGGAGTACCATTTATACT 58.187 43.478 0.00 0.00 43.89 2.12
4794 4951 4.831710 ACGGAGGGAGTACCATTTATACTC 59.168 45.833 0.00 3.98 45.28 2.59
4795 4952 4.082895 CGGAGGGAGTACCATTTATACTCG 60.083 50.000 0.00 0.00 46.43 4.18
4796 4953 4.220163 GGAGGGAGTACCATTTATACTCGG 59.780 50.000 0.00 0.00 46.43 4.63
4797 4954 3.577415 AGGGAGTACCATTTATACTCGGC 59.423 47.826 0.00 0.00 46.43 5.54
4798 4955 3.322828 GGGAGTACCATTTATACTCGGCA 59.677 47.826 6.18 0.00 46.43 5.69
4799 4956 4.020485 GGGAGTACCATTTATACTCGGCAT 60.020 45.833 6.18 0.00 46.43 4.40
4800 4957 5.512576 GGGAGTACCATTTATACTCGGCATT 60.513 44.000 6.18 0.00 46.43 3.56
4801 4958 6.295462 GGGAGTACCATTTATACTCGGCATTA 60.295 42.308 6.18 0.00 46.43 1.90
4802 4959 7.156673 GGAGTACCATTTATACTCGGCATTAA 58.843 38.462 6.18 0.00 46.43 1.40
4803 4960 7.658575 GGAGTACCATTTATACTCGGCATTAAA 59.341 37.037 6.18 0.00 46.43 1.52
4804 4961 8.603242 AGTACCATTTATACTCGGCATTAAAG 57.397 34.615 0.00 0.00 0.00 1.85
4805 4962 8.426489 AGTACCATTTATACTCGGCATTAAAGA 58.574 33.333 0.00 0.00 0.00 2.52
4806 4963 9.048446 GTACCATTTATACTCGGCATTAAAGAA 57.952 33.333 0.00 0.00 0.00 2.52
4807 4964 7.927048 ACCATTTATACTCGGCATTAAAGAAC 58.073 34.615 0.00 0.00 0.00 3.01
4840 4997 4.964593 TCCGCTGGGAAAAATATACCTAC 58.035 43.478 0.00 0.00 40.15 3.18
4842 4999 4.755123 CCGCTGGGAAAAATATACCTACAG 59.245 45.833 0.00 0.00 34.06 2.74
4843 5000 5.454187 CCGCTGGGAAAAATATACCTACAGA 60.454 44.000 0.00 0.00 34.06 3.41
4844 5001 5.465724 CGCTGGGAAAAATATACCTACAGAC 59.534 44.000 0.00 0.00 0.00 3.51
4845 5002 5.763698 GCTGGGAAAAATATACCTACAGACC 59.236 44.000 0.00 0.00 0.00 3.85
5003 5187 9.178758 ACTACTTTCCATGTCCATCTTAAATTC 57.821 33.333 0.00 0.00 0.00 2.17
5102 5286 6.305157 TCTGGCTTGAACAGTCTGGTACAG 62.305 50.000 4.53 2.76 45.59 2.74
5334 5528 1.356624 GGCGGCTCATGCAACATAC 59.643 57.895 0.00 0.00 41.91 2.39
5357 5551 3.326836 TGGTAAGCATGACATCAACGA 57.673 42.857 0.00 0.00 0.00 3.85
6301 6499 7.229506 AGCAAGAGCAGTTAAACATAAGAAACT 59.770 33.333 0.00 0.00 45.49 2.66
6356 6554 4.701651 CAGGATGAAATACAGGAAGTTGCA 59.298 41.667 0.00 0.00 39.69 4.08
6482 6910 4.793216 CAGAAACTCACAACTTTTTGGTCG 59.207 41.667 0.00 0.00 37.00 4.79
6945 7377 2.769663 AGCCACCGAGTGATACCAAATA 59.230 45.455 5.71 0.00 35.23 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 0.106894 GGGCTAGCTTTGTCGGCTAT 59.893 55.000 15.72 0.00 40.79 2.97
264 271 3.574284 TGTGGATTGCTGAAATTTCCG 57.426 42.857 15.48 10.32 0.00 4.30
270 277 5.774690 AGGTTCTATTTGTGGATTGCTGAAA 59.225 36.000 0.00 0.00 0.00 2.69
310 317 4.249661 GCCTGGTTCTCTCTGTTTCTTAG 58.750 47.826 0.00 0.00 0.00 2.18
315 322 1.072965 CCTGCCTGGTTCTCTCTGTTT 59.927 52.381 0.00 0.00 0.00 2.83
368 375 3.181483 CCTGGGCATGAAAGTTGCTATTC 60.181 47.826 0.00 0.00 40.03 1.75
380 387 0.981183 ACGTAGTTTCCTGGGCATGA 59.019 50.000 0.00 0.00 37.78 3.07
398 405 5.046910 TGCAGGTAAACGTGTAGTAGTAC 57.953 43.478 0.37 0.37 34.50 2.73
399 406 5.703978 TTGCAGGTAAACGTGTAGTAGTA 57.296 39.130 0.00 0.00 34.50 1.82
400 407 4.589216 TTGCAGGTAAACGTGTAGTAGT 57.411 40.909 0.00 0.00 34.50 2.73
401 408 5.636121 TGATTTGCAGGTAAACGTGTAGTAG 59.364 40.000 0.00 0.00 34.50 2.57
402 409 5.539979 TGATTTGCAGGTAAACGTGTAGTA 58.460 37.500 0.00 0.00 34.50 1.82
403 410 4.382291 TGATTTGCAGGTAAACGTGTAGT 58.618 39.130 0.00 0.00 34.50 2.73
404 411 5.049680 ACTTGATTTGCAGGTAAACGTGTAG 60.050 40.000 0.00 0.00 34.71 2.74
573 580 4.838486 CTCTCTGTCGGCGGCGAC 62.838 72.222 45.48 45.48 39.16 5.19
811 818 1.144057 GGTAGGTGTCGCCATGAGG 59.856 63.158 4.97 0.00 40.61 3.86
914 921 1.960417 GCTTAGAGCATTGGAGGGTC 58.040 55.000 0.00 0.00 41.89 4.46
961 972 4.278170 ACAATCTCGAGGAAAACAAATGCA 59.722 37.500 13.56 0.00 0.00 3.96
964 975 4.154195 CCGACAATCTCGAGGAAAACAAAT 59.846 41.667 13.56 0.00 46.14 2.32
967 978 2.297880 TCCGACAATCTCGAGGAAAACA 59.702 45.455 13.56 0.00 46.14 2.83
968 979 2.955614 TCCGACAATCTCGAGGAAAAC 58.044 47.619 13.56 1.44 46.14 2.43
1056 1068 8.758633 TTAGTTCTTGAAGCAAGTATGTAGAC 57.241 34.615 7.02 0.00 41.66 2.59
1154 1167 4.541310 TCCCATATCATCTGGCACCATATT 59.459 41.667 0.00 0.00 32.08 1.28
1158 1171 1.421268 GTCCCATATCATCTGGCACCA 59.579 52.381 0.00 0.00 32.08 4.17
1299 1312 3.014623 CTGCTTCAGATTCAGCCAATGA 58.985 45.455 0.00 0.00 34.91 2.57
1396 1410 2.756760 CCTTGTGAATGTGATCCAAGGG 59.243 50.000 13.80 0.00 45.38 3.95
1398 1412 3.689347 TCCCTTGTGAATGTGATCCAAG 58.311 45.455 0.00 0.00 33.88 3.61
1764 1778 6.197096 CGATCGCCCTGAAAGAAAATAAATTG 59.803 38.462 0.26 0.00 34.07 2.32
1766 1780 5.733373 GCGATCGCCCTGAAAGAAAATAAAT 60.733 40.000 29.48 0.00 32.22 1.40
1793 1807 9.289782 AGAACTTTATACTCTTCAACTTTGCAT 57.710 29.630 0.00 0.00 0.00 3.96
1871 1885 1.109323 GCAAGCTGGGGTGAACACTT 61.109 55.000 4.96 0.00 0.00 3.16
2076 2090 2.890945 GGTTCCTGGTGCTGTTTGTTAT 59.109 45.455 0.00 0.00 0.00 1.89
2111 2125 6.569179 TCTGTTTTGTACCTTTTGCTATCC 57.431 37.500 0.00 0.00 0.00 2.59
2112 2126 7.591426 CAGTTCTGTTTTGTACCTTTTGCTATC 59.409 37.037 0.00 0.00 0.00 2.08
2113 2127 7.284489 TCAGTTCTGTTTTGTACCTTTTGCTAT 59.716 33.333 0.00 0.00 0.00 2.97
2114 2128 6.600032 TCAGTTCTGTTTTGTACCTTTTGCTA 59.400 34.615 0.00 0.00 0.00 3.49
2115 2129 5.417580 TCAGTTCTGTTTTGTACCTTTTGCT 59.582 36.000 0.00 0.00 0.00 3.91
2116 2130 5.515270 GTCAGTTCTGTTTTGTACCTTTTGC 59.485 40.000 0.00 0.00 0.00 3.68
2159 2173 3.680458 GCGCAAGTCTAGCTTTAACTTCT 59.320 43.478 0.30 0.00 41.68 2.85
2344 2358 6.763610 AGTAGGTAGTTCTGCAAATTCTATGC 59.236 38.462 0.00 0.00 44.08 3.14
2666 2680 5.220491 GCTTGCTTTTAACTGATCTAGTCGG 60.220 44.000 0.00 0.00 39.18 4.79
2825 2839 7.954666 CCTTAAACAGAAGGGAATGGAATAA 57.045 36.000 0.00 0.00 42.12 1.40
3360 3374 4.517453 GCTCTCACCTCATCGTAGTAGAAT 59.483 45.833 0.00 0.00 0.00 2.40
3393 3407 4.770010 AGGGCGGAATTCTGTTTTTATTCA 59.230 37.500 15.63 0.00 31.47 2.57
3717 3731 4.283467 CCCTCCGATCCATATTACTTGTCA 59.717 45.833 0.00 0.00 0.00 3.58
3768 3782 7.891183 ATACATAAGATGAACCGTCATTAGC 57.109 36.000 0.00 0.00 44.83 3.09
4036 4180 9.434420 TGCTTGTTCATAATTTTTATTTGGGAG 57.566 29.630 0.00 0.00 0.00 4.30
4084 4228 5.877012 GCATGACTAAATGTCCTTCAAGAGA 59.123 40.000 0.00 0.00 44.75 3.10
4085 4229 5.645067 TGCATGACTAAATGTCCTTCAAGAG 59.355 40.000 0.00 0.00 44.75 2.85
4258 4415 9.743057 TTCAGTTGTTGGATTTATTGTTTACTG 57.257 29.630 0.00 0.00 0.00 2.74
4269 4426 7.346751 AGTATGTTGTTCAGTTGTTGGATTT 57.653 32.000 0.00 0.00 0.00 2.17
4284 4441 8.149973 AGTTCGTCATTTTACAAGTATGTTGT 57.850 30.769 1.41 1.41 41.05 3.32
4674 4831 2.237393 TGCCTGTTTGCCATTTGTTC 57.763 45.000 0.00 0.00 0.00 3.18
4746 4903 7.225931 GTCCCATAATATAAGAGCGTGTCAAAA 59.774 37.037 0.00 0.00 0.00 2.44
4748 4905 6.220930 GTCCCATAATATAAGAGCGTGTCAA 58.779 40.000 0.00 0.00 0.00 3.18
4749 4906 5.564063 CGTCCCATAATATAAGAGCGTGTCA 60.564 44.000 0.00 0.00 0.00 3.58
4750 4907 4.857588 CGTCCCATAATATAAGAGCGTGTC 59.142 45.833 0.00 0.00 0.00 3.67
4751 4908 4.321750 CCGTCCCATAATATAAGAGCGTGT 60.322 45.833 0.00 0.00 0.00 4.49
4752 4909 4.082408 TCCGTCCCATAATATAAGAGCGTG 60.082 45.833 0.00 0.00 0.00 5.34
4753 4910 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
4754 4911 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
4755 4912 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
4756 4913 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
4757 4914 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
4758 4915 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
4759 4916 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
4760 4917 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4761 4918 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4762 4919 3.501019 GGTACTCCCTCCGTCCCATAATA 60.501 52.174 0.00 0.00 0.00 0.98
4763 4920 2.606378 GTACTCCCTCCGTCCCATAAT 58.394 52.381 0.00 0.00 0.00 1.28
4764 4921 1.412074 GGTACTCCCTCCGTCCCATAA 60.412 57.143 0.00 0.00 0.00 1.90
4765 4922 0.186873 GGTACTCCCTCCGTCCCATA 59.813 60.000 0.00 0.00 0.00 2.74
4766 4923 1.075450 GGTACTCCCTCCGTCCCAT 60.075 63.158 0.00 0.00 0.00 4.00
4767 4924 1.882189 ATGGTACTCCCTCCGTCCCA 61.882 60.000 0.00 0.00 0.00 4.37
4768 4925 0.690077 AATGGTACTCCCTCCGTCCC 60.690 60.000 0.00 0.00 0.00 4.46
4769 4926 1.201424 AAATGGTACTCCCTCCGTCC 58.799 55.000 0.00 0.00 0.00 4.79
4770 4927 4.831710 AGTATAAATGGTACTCCCTCCGTC 59.168 45.833 0.00 0.00 0.00 4.79
4771 4928 4.812653 AGTATAAATGGTACTCCCTCCGT 58.187 43.478 0.00 0.00 0.00 4.69
4772 4929 4.082895 CGAGTATAAATGGTACTCCCTCCG 60.083 50.000 7.49 0.00 43.17 4.63
4773 4930 4.220163 CCGAGTATAAATGGTACTCCCTCC 59.780 50.000 7.49 0.00 43.17 4.30
4774 4931 4.321824 GCCGAGTATAAATGGTACTCCCTC 60.322 50.000 7.49 0.00 43.17 4.30
4775 4932 3.577415 GCCGAGTATAAATGGTACTCCCT 59.423 47.826 7.49 0.00 43.17 4.20
4776 4933 3.322828 TGCCGAGTATAAATGGTACTCCC 59.677 47.826 7.49 1.48 43.17 4.30
4777 4934 4.595762 TGCCGAGTATAAATGGTACTCC 57.404 45.455 7.49 0.00 43.17 3.85
4778 4935 8.597662 TTTAATGCCGAGTATAAATGGTACTC 57.402 34.615 3.78 3.78 42.84 2.59
4779 4936 8.426489 TCTTTAATGCCGAGTATAAATGGTACT 58.574 33.333 0.00 0.00 35.20 2.73
4780 4937 8.597662 TCTTTAATGCCGAGTATAAATGGTAC 57.402 34.615 0.00 0.00 0.00 3.34
4781 4938 9.048446 GTTCTTTAATGCCGAGTATAAATGGTA 57.952 33.333 0.00 0.00 0.00 3.25
4782 4939 7.554835 TGTTCTTTAATGCCGAGTATAAATGGT 59.445 33.333 0.00 0.00 0.00 3.55
4783 4940 7.925993 TGTTCTTTAATGCCGAGTATAAATGG 58.074 34.615 0.00 0.00 0.00 3.16
4784 4941 9.781834 TTTGTTCTTTAATGCCGAGTATAAATG 57.218 29.630 0.00 0.00 0.00 2.32
4785 4942 9.783256 GTTTGTTCTTTAATGCCGAGTATAAAT 57.217 29.630 0.00 0.00 0.00 1.40
4786 4943 8.784994 TGTTTGTTCTTTAATGCCGAGTATAAA 58.215 29.630 0.00 0.00 0.00 1.40
4787 4944 8.325421 TGTTTGTTCTTTAATGCCGAGTATAA 57.675 30.769 0.00 0.00 0.00 0.98
4788 4945 7.908827 TGTTTGTTCTTTAATGCCGAGTATA 57.091 32.000 0.00 0.00 0.00 1.47
4789 4946 6.811253 TGTTTGTTCTTTAATGCCGAGTAT 57.189 33.333 0.00 0.00 0.00 2.12
4790 4947 6.621316 TTGTTTGTTCTTTAATGCCGAGTA 57.379 33.333 0.00 0.00 0.00 2.59
4791 4948 5.508200 TTGTTTGTTCTTTAATGCCGAGT 57.492 34.783 0.00 0.00 0.00 4.18
4792 4949 5.977129 ACTTTGTTTGTTCTTTAATGCCGAG 59.023 36.000 0.00 0.00 0.00 4.63
4793 4950 5.897050 ACTTTGTTTGTTCTTTAATGCCGA 58.103 33.333 0.00 0.00 0.00 5.54
4794 4951 7.061789 GGATACTTTGTTTGTTCTTTAATGCCG 59.938 37.037 0.00 0.00 0.00 5.69
4795 4952 7.061789 CGGATACTTTGTTTGTTCTTTAATGCC 59.938 37.037 0.00 0.00 0.00 4.40
4796 4953 7.410407 GCGGATACTTTGTTTGTTCTTTAATGC 60.410 37.037 0.00 0.00 0.00 3.56
4797 4954 7.807907 AGCGGATACTTTGTTTGTTCTTTAATG 59.192 33.333 0.00 0.00 0.00 1.90
4798 4955 7.807907 CAGCGGATACTTTGTTTGTTCTTTAAT 59.192 33.333 0.00 0.00 0.00 1.40
4799 4956 7.136119 CAGCGGATACTTTGTTTGTTCTTTAA 58.864 34.615 0.00 0.00 0.00 1.52
4800 4957 6.293735 CCAGCGGATACTTTGTTTGTTCTTTA 60.294 38.462 0.00 0.00 0.00 1.85
4801 4958 5.507315 CCAGCGGATACTTTGTTTGTTCTTT 60.507 40.000 0.00 0.00 0.00 2.52
4802 4959 4.023193 CCAGCGGATACTTTGTTTGTTCTT 60.023 41.667 0.00 0.00 0.00 2.52
4803 4960 3.502211 CCAGCGGATACTTTGTTTGTTCT 59.498 43.478 0.00 0.00 0.00 3.01
4804 4961 3.365969 CCCAGCGGATACTTTGTTTGTTC 60.366 47.826 0.00 0.00 0.00 3.18
4805 4962 2.556622 CCCAGCGGATACTTTGTTTGTT 59.443 45.455 0.00 0.00 0.00 2.83
4806 4963 2.159382 CCCAGCGGATACTTTGTTTGT 58.841 47.619 0.00 0.00 0.00 2.83
4807 4964 2.432444 TCCCAGCGGATACTTTGTTTG 58.568 47.619 0.00 0.00 31.13 2.93
4837 4994 4.820897 TGAAATGCACACTAGGTCTGTAG 58.179 43.478 0.00 0.00 0.00 2.74
4840 4997 3.005554 CCTGAAATGCACACTAGGTCTG 58.994 50.000 0.00 0.00 0.00 3.51
4842 4999 1.740025 GCCTGAAATGCACACTAGGTC 59.260 52.381 9.74 1.19 0.00 3.85
4843 5000 1.826385 GCCTGAAATGCACACTAGGT 58.174 50.000 9.74 0.00 0.00 3.08
4844 5001 0.729116 CGCCTGAAATGCACACTAGG 59.271 55.000 0.00 0.00 0.00 3.02
4845 5002 0.097674 GCGCCTGAAATGCACACTAG 59.902 55.000 0.00 0.00 0.00 2.57
5003 5187 6.444633 TCACTTTCAGGTTCTTACTAGTTCG 58.555 40.000 0.00 0.00 0.00 3.95
5102 5286 5.575606 CCTGAATGTGCATGAGTTTTGAATC 59.424 40.000 0.00 0.00 0.00 2.52
5334 5528 3.302675 CGTTGATGTCATGCTTACCATCG 60.303 47.826 0.00 0.00 37.18 3.84
5357 5551 6.610075 AACAACATAAAATTGGAGGCTGAT 57.390 33.333 0.00 0.00 0.00 2.90
5441 5636 0.105760 TTCCAAAAGGGGAAGCTGCA 60.106 50.000 1.02 0.00 41.92 4.41
5961 6156 5.762179 TCTAATGAGGCCAGAAAGAAAGA 57.238 39.130 5.01 0.00 0.00 2.52
6301 6499 3.306472 AAAAGGGTGACTGTTTGCCTA 57.694 42.857 0.00 0.00 0.00 3.93


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.